Isolation of a Novel Phage with Activity against Streptococcus mutans Biofilms

peer-reviewedStreptococcus mutans is one of the principal agents of caries formation mainly, because of its ability to form biofilms at the tooth surface. Bacteriophages (phages) are promising antimicrobial agents that could be used to prevent or treat caries formation by S. mutans. The aim of this study was to isolate new S. mutans phages and to characterize their antimicrobial properties. A new phage, ɸAPCM01, was isolated from a human saliva sample. Its genome was closely related to the only two other available S. mutans phage genomes, M102 and M102AD. ɸAPCM01 inhibited the growth of S. mutans strain DPC6143 within hours in broth and in artificial saliva at multiplicity of infections as low as 2.5x10-5. In the presence of phage ɸAPCM01 the metabolic activity of a S. mutans biofilm was reduced after 24 h of contact and did not increased again after 48 h, and the live cells in the biofilm decreased by at least 5 log cfu/ml. Despite its narrow host range, this newly isolated S. mutans phage exhibits promising antimicrobial properties

Thermal Instability and Photoionized X-ray Reflection in Accretion Disks

We study the X-ray illumination of an accretion disk. We relax the simplifying assumption of constant gas density used in most previous studies; instead we determine the density from hydrostatic balance. It is found that the thermal ionization instability prevents the illuminated gas from attaining temperatures at which the gas is unstable. In particular, the uppermost layers of the X-ray illuminated gas are found to be almost completely ionized and at the local Compton temperature ($\sim 10^7 - 10^8$ K); at larger depths, the gas temperature drops abruptly to form a thin layer with $T\sim 10^6$ K, while at yet larger depths it decreases sharply to the disk effective temperature. We find that most of the Fe K$\alpha$ line emission and absorption edge are produced in the coolest, deepest layers, while the Fe atoms in the hottest, uppermost layers are generally almost fully ionized, hence making a negligible contribution to reprocessing features in $\sim 6.4-10$ keV energy range. We provide a summary of how X-ray reprocessing features depend on parameters of the problem. The results of our self-consistent calculations are both quantitatively and qualitatively different from those obtained using the constant density assumption. Therefore, we conclude that X-ray reflection calculations should always utilize hydrostatic balance in order to provide a reliable theoretical interpretation of observed X-ray spectra of AGN and GBHCs.Comment: Submitted to ApJ; 16 pages plus 13 figure

Strings in extremal BTZ black holes

We study the spectrum of the worldsheet theory of the bosonic closed string in the massless and extremal rotating BTZ black holes. We use a hyperbolic Wakimoto representation of the SL(2,R) currents to construct vertex operators for the string modes on these backgrounds. We argue that there are tachyons in the twisted sector, but these are not localised near the horizon. We study the relation to the null orbifold in the limit of vanishing cosmological constant. We also discuss the problem of extending this analysis to the supersymmetric case.Comment: 20 pages, no figure

Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle

The Rowett Institute of Nutrition and Health and SRUC are funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The project was supported by DEFRA and DA funded Agricultural Greenhouse Gas Inventory Research Platform. Our thanks are due to the excellent support staff at the SRUC Beef Research Centre, Edinburgh, also to Graham Horgan of BioSS, Aberdeen, for conducting multivariate analysis.Peer reviewedPublisher PD

Thermodynamics of Chemical Waves

Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a rigorous thermodynamic theory of reaction-diffusion systems to characterize chemical waves. Our main result is the definition of the proper thermodynamic potential of the local dynamics as a nonequilibrium free energy density and establishing its balance equation. This enables us to identify the dynamics of the free energy, of the dissipation, and of the work spent to sustain the wave propagation. Two prototypical classes of chemical waves are examined. From a thermodynamic perspective, the first is sustained by relaxation towards equilibrium and the second by nonconservative forces generated by chemostats. We analytically study step-like waves, called wavefronts, using the Fisher-Kolmogorov equation as representative of the first class and oscillating waves in the Brusselator model as representative of the second. Given the fundamental role of chemical waves as message carriers in biosystems, our thermodynamic theory constitutes an important step toward an understanding of information transfers and processing in biology.Comment: 12 pages, 2 figure

Double-heterostructure cavities: from theory to design

We derive a frequency-domain-based approach for radiation (FAR) from double-heterostructure cavity (DHC) modes. We use this to compute the quality factors and radiation patterns of DHC modes. The semi-analytic nature of our method enables us to provide a general relationship between the radiation pattern of the cavity and its geometry. We use this to provide general designs for ultrahigh quality factor DHCs with radiation patterns that are engineered to emit vertically

Global hydrodynamic analysis of the molecular flexibility of galactomannans

In the past, intrinsic viscosity and sedimentation velocity analyses have been used separately to assess the conformation and flexibility of guar and locust bean gum galactomannans based on worm-like chain and semi-flexible coil models. Publication of a new global method combining data sets of both intrinsic viscosity and sedimentation coefficient with molecular weight, and minimising a target (error) function now permits a more robust analysis. Using this approach, values for the persistence length of (10 ± 2) nm for guar and (7 ± 1) nm for locust bean gum are returned if the mass per unit length ML is floated as a variable. Using a fixed mass per unit length based on the known compositional data of each galactomannan yields a similar value for Lp in both cases, (8 ± 1) nm for guar and (9 ± 1) nm for locust bean gum, with combined set of data yielding (9 ± 1) nm: within experimental error the flexibilities of both galactomannans are very similar. © 2007 Elsevier Ltd. All rights reserved

A functional-cognitive framework for attitude research

In attitude research, behaviours are often used as proxies for attitudes and attitudinal processes. This practice is problematic because it conflates the behaviours that need to be explained (explanandum) with the mental constructs that are used to explain these behaviours (explanans). In the current chapter we propose a meta-theoretical framework that resolves this problem by distinguishing between two levels of analysis. According to the proposed framework, attitude research can be conceptualised as the scientific study of evaluation. Evaluation is defined not in terms of mental constructs but in terms of elements in the environment, more specifically, as the effect of stimuli on evaluative responses. From this perspective, attitude research provides answers to two questions: (1) Which elements in the environment moderate evaluation? (2) What mental processes and representations mediate evaluation? Research on the first question provides explanations of evaluative responses in terms of elements in the environment (functional level of analysis); research on the second question offers explanations of evaluation in terms of mental processes and representations (cognitive level of analysis). These two levels of analysis are mutually supportive, in that better explanations at one level lead to better explanations at the other level. However, their mutually supportive relation requires a clear distinction between the concepts of their explanans and explanandum, which are conflated if behaviours are treated as proxies for mental constructs. The value of this functional-cognitive framework is illustrated by applying it to four central questions of attitude research

Solitons in Five Dimensional Minimal Supergravity: Local Charge, Exotic Ergoregions, and Violations of the BPS Bound

We describe a number of striking features of a class of smooth solitons in gauged and ungauged minimal supergravity in five dimensions. The solitons are globally asymptotically flat or asymptotically AdS without any Kaluza-Klein directions but contain a minimal sphere formed when a cycle pinches off in the interior of the spacetime. The solutions carry a local magnetic charge and many have rather unusual ergosurfaces. Perhaps most strikingly, many of the solitons have more electric charge or, in the asymptotically AdS case, more electric charge and angular momentum than is allowed by the usual BPS bound. We comment on, but do not resolve, the new puzzle this raises for AdS/CFT.Comment: 60 pages, 12 figures, 3 table